Despite being a protected National Park, approximately 65% of the park's primary forest is degraded. It is the loss of natural habitat that is the greatest threat to the wildlife. Friends of National Parks Foundation is an Indonesian NGO that has been working to restore the habitat in the Pasalat and Beguruh regions of the park since 1997. It also operates a conservation education centre in Pasalat.

Four research centers have been established within the park for the study and rehabilitation of orangutans and other primates. Camp Leakey, founded in 1971 with assistance from the Leakey Foundation, was the first of these centers. It was here where Dr. Birute Galdikas began her career studying the behavior of rescued and orphaned orangutans that were reintroduced into the wild. Her research was highlighted as the cover article of National Geographic in October 1975. Dr. Galdikas is now considered one of the world’s leading experts on orangutan behaviour and is the founder and president of the Orangutan Foundation International.

Today Tanjung Puting National Park is a popular ecotourism destination, with many local tour companies offering multi-day boat tours to view wildlife and visit the research centers. The park was home to 105,000 people as of 1997.[3] The park was heavily damaged by fires in 1997 and 1998, and today remains threatened by illegal logging, illegal mining, and forest clearing for agricultural uses.

Conservation efforts by Indonesian NGO Friends of the National Parks Foundation is leading towards a slow but progressive reforestation of damaged areas. Their reforestation work has seen the planting of thousands of saplings in the area to recreate habitat for the endemic wildlife in the area.